plotSpliceEvent {ribosomeProfilingQC} | R Documentation

## Plot splice event

### Description

Plot the splice event

### Usage

    plotSpliceEvent(
      se,
      tx_name,
      coverage,
      group1,
      group2,
      cutoffFDR = 0.05,
      resetIntronWidth = TRUE
    )

### Arguments

`se` | Output of spliceEvent
`tx_name` | Transcript name.
`coverage` | Coverages of feature region with extensions. Output of coverageDepth
`group1, group2` | The sample names of group 1 and group 2
`cutoffFDR` | Cutoff of FDR
`resetIntronWidth` | logical(1). If set to true, reset the region with no read to minimal width.

### Value

A ggplot object.

### Examples

    ## Not run:
    path <- system.file("extdata", package="ribosomeProfilingQC")
    RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
    gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
    coverage <- coverageDepth(RPFs, gtf=gtf, level="gene",
                              region="feature with extension")
    group1 <- c("RPF.KD1.1", "RPF.KD1.2")
    group2 <- c("RPF.WT.1", "RPF.WT.2")
    se <- spliceEvent(coverage, group1, group2)
    plotSpliceEvent(se, se$feature[1], coverage, group1, group2)

    ## End(Not run)

[Package ribosomeProfilingQC version 0.99.9 Index]